Department of Biochemistry, University of Oxford, Oxford, UK.
MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
Life Sci Alliance. 2021 Nov 30;5(2). doi: 10.26508/lsa.202101111. Print 2022 Feb.
The nuclear RNA exosome plays a key role in controlling the levels of multiple protein-coding and non-coding RNAs. Recruitment of the exosome to specific RNA substrates is mediated by RNA-binding co-factors. The transient interaction between co-factors and the exosome as well as the rapid decay of RNA substrates make identification of exosome co-factors challenging. Here, we use comparative poly(A)+ RNA interactome capture in fission yeast expressing three different mutants of the exosome to identify proteins that interact with poly(A)+ RNA in an exosome-dependent manner. Our analyses identify multiple RNA-binding proteins whose association with RNA is altered in exosome mutants, including the zinc-finger protein Mub1. Mub1 is required to maintain the levels of a subset of exosome RNA substrates including mRNAs encoding for stress-responsive proteins. Removal of the zinc-finger domain leads to loss of RNA suppression under non-stressed conditions, altered expression of heat shock genes in response to stress, and reduced growth at elevated temperature. These findings highlight the importance of exosome-dependent mRNA degradation in buffering gene expression networks to mediate cellular adaptation to stress.
核 RNA 外切酶在控制多种蛋白质编码和非编码 RNA 的水平方面发挥着关键作用。外切酶对特定 RNA 底物的募集是由 RNA 结合共因子介导的。共因子与外切酶之间的瞬时相互作用以及 RNA 底物的快速降解使得外切酶共因子的鉴定具有挑战性。在这里，我们使用裂殖酵母中表达三种不同外切酶突变体的比较多聚(A)+ RNA 免疫沉淀技术，鉴定以外切酶依赖方式与多聚(A)+ RNA 相互作用的蛋白质。我们的分析确定了多个 RNA 结合蛋白，它们与 RNA 的结合在外切酶突变体中发生改变，包括锌指蛋白 Mub1。Mub1 对于维持包括应激反应蛋白编码 mRNA 在内的一组外切酶 RNA 底物的水平是必需的。去除锌指结构域会导致在非应激条件下失去 RNA 抑制，应激时热休克基因的表达改变，以及在高温下生长减少。这些发现强调了外切酶依赖的 mRNA 降解在缓冲基因表达网络以介导细胞对应激的适应中的重要性。
